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Python library for hierarchy of ICD9 Codes
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README.md

Python library for ICD9 Codes

The library encodes ICD9 codes in their natural hierarchy. For example, "Cholera due to vibrio cholerae" has the ICD9 code 001.0, and is categorized as a type of Cholera, which in turn is a type of Intestinal Infectious Disease. Specifically, 001.0 has the following hierarchy:

001-139     Infectious and Parasitic Diseases
  001-009   Intestinal Infectious Diseases
    001     Cholera
      001.0 Cholera due to vibrio cholerae

Assuming that codes closely related in the tree are more related than with codes further in the tree, this hierarchy is a way to cluster related codes.

This library encodes all ICD9 codes and their descriptions into a tree that captures these relationships.

Using the library

Include icd9.py in your python path. Then put codes.json somewhere convenient. Here's a simple example:

from icd9 import ICD9

# feel free to replace with your path to the json file
tree = ICD9('codes.json')

# list of top level codes (e.g., '001-139', ...)
toplevelnodes = tree.children
toplevelcodes = [node.code for node in toplevelnodes]
print '\t'.join(toplevelcodes)

The hierarchy is encoded in a tree of Node objects. The ICD9() constructor returns the root Node. Node has the following methods:

node.search(code)

# find all sub-nodes whose codes contain '001'
tree.search('001')

node.find(code)

# find sub-node with code '001.0'. Returns None if code is not found
tree.find('001.0')

And the following properties:

node.code

# get node's ICD9 code
tree.find('001.1').code

# prints '001'
tree.find('001.1').parent.code

# prints '001'
tree.find('001').code

node.description:

# get english description of ICD9 code
# prints: 'Cholera due to vibrio cholerae el tor'
tree.find('001.1').description

# prints: 'ROOT'
tree.description

# prints: 'Cholera'
tree.find('001.1').parent.description

# also prints: 'Cholera'
tree.find('001').description

node.descr: alias for description

node.children

# get node's children
tree.children

# search for '001.0' in root's first child
tree.children[0].search('001.0')

node.parent

# get 001.0 node's parent.  None if node is a root
tree.find('001.0').parent

node.parents

# get 001.0 node's parent path from the root.  Root node is the first element
tree.find('001.0').parents

node.leaves

# get all leaf nodes under root's first child
tree.children[0].leaves

node.siblings

# get all of 001.0 node's siblings that share the same parent
tree.find('001.0').siblings

ICD9 Descriptions

This library includes descriptions of each ICD9 code and grouping name.

If you are interested in another list of ICD9 codes and their descriptions, drobhbins created a csv file of ICD9 codes and their short and long descriptions.

Scraper

The scraper/ directory includes the scraper code used to generate the dataset. scraper/scraper.py creates a json file codes.json of each ICD9 code's parent codes and descriptions:

[
  {'code': None},
  {'code': '001-139', 'descr': 'Infectious and Parasitic Diseases'},
  {'code': '001-009', 'descr': 'Intestinal Infectious Diseases'},
  {'code': '001', 'descr': 'Cholera'},
  {'code':  '001.0', 'descr': 'Cholera due to vibrio cholerae'}
]

The last element is the actual code, the preceeding elements are coarser groupings of codes. The first element is a dummy that represents root.

Thanks to http://icd9cm.chrisendres.com/, where the data was secretly scraped from.

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